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01.

medRxiv (Medicine) 2026-06-18 DOI: HASH:978670384e849196db5d532e4702fbe7

Urinary Creatine Riboside Complements PSA to Improve Disease Detection in the Diagnostic Gray Zone of Prostate Cancer

作者:

Patel↗D. P↗Casiano↗A. S↗Toulabi↗Khan↗Dorsey↗T. H↗Mathe↗E. A↗Harris↗C. C↗…

Circulating prostate-specific antigen (PSA) discriminates poorly in the diagnostic gray zone (3.0-9.99 ng/mL), where ~75% of biopsies yield no clinically significant prostate cancer (PCa). We evaluated whether urinary creatine riboside (CR), a tumor-derived metabolite excreted through the prostatic urethra, complements PSA for gray-zone detection and independently predicts prostate-cancer-specific mortality (PCSM). In the NCI-Maryland PCa Case-Control Study (951 cases, 962 controls; 47.6% African American men; median follow-up 11.5 years), urinary CR was quantified by UPLC-MS/MS. Within the PSA gray zone (n = 668), urinary CR was complementary to PSA, with markedly higher single-marker discrimination than PSA (AUC 0.93, 95% CI 0.88-0.98 vs 0.77, 0.66-0.89) and additive when combined ({Delta}AUC +0.17, p < 0.001; 91.4% sensitivity at 80% specificity). After adjustment for 11 clinical and sociodemographic covariates, urinary CR independently predicted PCSM complementary to PSA (Fine-Gray SHR 1.72, 1.35-2.19 for CR; 1.35, 1.08-1.68 for PSA; Harrell's C 0.85 for CR + PSA vs 0.77 for PSA alone), with strongest signal in African American men (SHR 2.43, 1.57-3.75 for CR). We conclude that urinary CR is a candidate non-invasive biomarker complementary to PSA - improving gray-zone triage and predicting PCSM; prospective validation in biopsy-referred cohorts is warranted.

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02.

arXiv (CS.CL) 2026-06-12 DOI: arXiv:2606.13477

SupraBench: A Benchmark for Supramolecular Chemistry

作者:

Tianyi Ma↗Yijun Ma↗Zehong Wang↗Weixiang Sun↗Ziming Li↗Connor R. Schmidt↗Chuxu Zhang↗Matthew J. Webber↗Yanfang Ye↗

Supramolecular chemistry, which includes the study of non-covalent host-guest assemblies, has advanced various applications. However, designing host-guest systems remains time-consuming, requiring days of dry-lab verification per candidate pair. Although LLMs have emerged as a fast alternative with strong performance on molecular binding tasks, no benchmark currently systematically evaluates LLMs for host-guest reasoning across fundamental supramolecular chemistry tasks, e.g., binding affinity prediction. To this end, we collaborate with domain experts to release the first Supramolecular Benchmark, called SupraBench, to evaluate LLMs in chemistry reasoning. Specifically, we design four fundamental tasks, i.e., binding affinity prediction, top-binder selection, solvent identification, and host-guest description, plus an auxiliary vision-based task for molecular identification. We also release SupraPMC, a curated 16M-token corpus of Supramolecular chemistry articles distilled from Europe PMC, to support the adaptation to the supramolecular domain. We benchmark a broad range of open and proprietary LLMs and find that LLMs leave substantial headroom across all tasks. Domain adaptation pretraining over SupraPMC transfers cleanly to in-distribution regression but trades off against strict letter-format output. Moreover, the difficulty profile differs sharply across task families, revealing distinct failure modes that indicate specific gaps in current supramolecular chemistry reasoning. Our source codes and benchmark datasets are available at https://github.com/Tianyi-Billy-Ma/SupraBench.

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03.

arXiv (CS.AI) 2026-06-18 DOI: arXiv:2507.04219

Model Collapse Is Not a Bug but a Feature in Machine Unlearning for LLMs

作者:

Yan Scholten↗Sophie Xhonneux↗Leo Schwinn↗Stephan G\"unnemann↗

arXiv:2507.04219v5 Announce Type: replace-cross Abstract: Current unlearning methods for LLMs optimize on the private information they seek to remove by incorporating it into their fine-tuning data. We argue this not only risks reinforcing exposure to sensitive data, but also fundamentally contradicts the principle of minimizing its use. As a remedy, we propose a novel unlearning method-Partial Model Collapse (PMC), which does not require unlearning targets in the unlearning objective. Our approach is inspired by recent observations that training generative models on their own generations leads to distribution collapse, effectively removing information from model outputs. Our central insight is that model collapse can be leveraged for machine unlearning by deliberately triggering it for data we aim to remove. We theoretically analyze that our approach converges to the desired outcome, i.e. the model unlearns the data targeted for removal. We empirically demonstrate that PMC overcomes four key limitations of existing unlearning methods that explicitly optimize on unlearning targets, and more effectively removes private information from model outputs while preserving general model utility. Overall, our contributions represent an important step toward more comprehensive unlearning that better aligns with real-world privacy constraints. Code available at https://www.cs.cit.tum.de/daml/partial-model-collapse/.

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04.

arXiv (CS.LG) 2026-06-16 DOI: arXiv:2606.15751

Acoustic Prompting via Stage-wise Modulation for Few-Shot Learning in Audio Language Models

作者:

Hyebin Cho↗Jaehyuk Jang↗Changick Kim↗Joon Son Chung↗

arXiv:2606.15751v1 Announce Type: cross Abstract: Audio-Language Models (ALMs) have shown remarkable success in zero-shot audio classification by aligning audio waveforms with text. Recent efforts to improve downstream performance focus on learning optimal text prompts. However, previous approaches focus on the text encoder, leaving the potential of learnable prompts within the audio encoder unexplored. In this paper, we propose a novel framework that introduces trainable prompts into the audio encoder to capture task-specific acoustic features. We demonstrate that integrating audio-side prompt learning with existing text-side approaches enhances few-shot adaptation. Through extensive experiments across 11 datasets show that integrating our method as a plug-and-play module alongside existing text prompt tuning generally leads to performance improvements. These findings suggest that explicitly modulating the audio representation space effectively complements text-only prompting approaches. The code is available at https://github.com/hyebin-c/aspl.

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05.

PLOS Medicine 2026-05-13 DOI: HASH:09e1b7c2032e6adf96b8b52c7c1c674e

Contribution of nosocomial transmission to <i>Klebsiella pneumoniae</i> neonatal sepsis in Africa and South Asia: An observational study of infection clusters inferred from pathogen genomics and temporal data

作者:

Erkison Ewomazino Odih↗

by Erkison Ewomazino Odih, Jabir A. Abdulahi, Anne V. Amulele, Matthew Bates, Eva Heinz, Weiming Hu, Kajal Jain, Rindidzani Magobo, Courtney P. Olwagen, John M. Tembo, Tolbert Sonda, Jonathan Strysko, Caroline C. Tigoi, Kyle Bittinger, Jennifer Cornick, Ebenezer Foster-Nyarko, Wilson Gumbi, Steven M. Jones, Chileshe L. Musyani, Carolyn M. McGann, Ahmed M. Moustafa, Patrick Musicha, James C. L. Mwansa, Moreka L. Ndumba, Thomas D. Stanton, Donwilliams O. Omuoyo, Oliver Pearse, Laura T. Phillips, Paul J. Planet, Charlene M. C. Rodrigues, Fatou Secka, Kirsty Sands, Erin Theiller, Allan M. Zuza, Sulagna Basu, Grace J. Chan, Kenneth C. Iregbu, Jean-Baptiste Mazarati, Semaria Solomon Alemayehu, Timothy R. Walsh, Rabaab Zahra, Angela Dramowski, Sombo Fwoloshi, Appiah-Korang Labi, Lola Madrid, Noah Obeng-Nkrumah, David Ojok, Boaz D. Wadugu, Andrew C. Whitelaw, Anudita Bhargava, Atul Jindal, Ramesh K. Agarwal, Alexander M. Aiken, James A. Berkley, Susan E. Coffin, Nicholas A. Feasey, Nelesh P. Govender, Davidson H. Hamer, Shabir A. Madhi, Mari Jeeva Sankar, Kelly L. Wyres, Kathryn E. Holt Background Klebsiella pneumoniae is the leading cause of sepsis among neonates in low- and middle-income countries (LMICs) in Africa and Asia, contributing substantially to the overall burden of antimicrobial-resistant infections and mortality among neonates globally. Pathogen sequencing has been used to investigate case clusters and confirm nosocomial transmission in a small number of neonatal units. Here we utilise pathogen sequence data to estimate the fraction of K. pneumoniae neonatal sepsis attributable to nosocomial transmission in African and South Asian countries. Methods and findings We estimated the proportion of invasive K. pneumoniae disease involved in nosocomial transmission clusters in a given neonatal unit, using single-linkage clustering based on pairwise temporal and genetic distances estimated from bacterial whole-genome sequences aggregated from 10 contributing studies. Analysing 1,523 K. pneumoniae isolates from 27 units in 13 countries in Africa and South Asia between 2013 and 2023, we inferred 156 nosocomial transmission clusters, ranging from 2 to 188 neonates each (83 of the clusters comprised ≥3 cases). Overall, we estimated that 1,035 neonatal infections (68.0%) were part of nosocomial transmission clusters. Excluding the first infection in each cluster as a potential index case, we estimate at least 879 (57.7%) infections were acquired via nosocomial transmission. Sensitivity analyses showed that results were robust to the choice of genetic distance estimation methods and thresholds used to define clusters, and cluster estimates were stable over temporal distance thresholds ranging from 2 to 8 weeks. Isolates were mostly extended-spectrum beta-lactamase (ESBL) producers (90.9%) and included 172 multi-locus sequence types (STs). Fourteen STs, including several globally recognised multidrug-resistant lineages, were associated with transmission clusters at multiple units, and these were collectively responsible for two-thirds of all infections. Carriage of carbapenemase genes (adjusted odds ratio, aOR = 2.08 [95% confidence interval, CI: 1.04, 4.14]; p = 0.04) and ESBL genes (aOR = 2.48 [95% CI: 1.26, 4.90]; p = 0.006) were significantly positively associated with transmission in a logistic regression model with site as a covariate. Limitations of this study include the lack of sufficient clinical data to allow high-resolution investigation of transmission dynamics and lack of facility-level data to investigate contributors to the observed differences in transmission burden across sites. Conclusions Nosocomial transmission contributes to a substantial proportion of K. pneumoniae sepsis in neonatal care units in Africa and South Asia. Reducing transmission within these settings through improved infection prevention and control and other measures could substantially reduce the neonatal sepsis burden. A high burden of transmission clusters is associated with the same drug-resistant lineages that are recognised as high-risk clones associated with hospital outbreaks in high-income countries, indicating global connectivity of the antimicrobial-resistant pathogen population.

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06.

arXiv (CS.LG) 2026-06-16 DOI: arXiv:2606.15356

ShipNet: A Geometric Deep Learning Surrogate for Real-Time Ship Hydrodynamics

作者:

Kirsten Odendaal↗George Drakoulas↗

arXiv:2606.15356v1 Announce Type: cross Abstract: Accurate prediction of hydrodynamic performance is central to ship design, yet high-fidelity computational fluid dynamics remains prohibitively expensive for large-scale parametric exploration. This motivates the development of data-driven surrogate models that provide rapid approximations to hydrodynamic predictions at substantially reduced cost. We present ShipNet, a geometric deep-learning surrogate that predicts both hull-surface pressure distributions and far-field free-surface wave patterns directly from hull geometry and speed. The network employs a regularized dynamic graph convolutional backbone on hull point clouds, with a multi-head decoder for simultaneous near-body pressure and free-surface elevation outputs. Training data consist of 420 inviscid free-surface simulations generated using a potential-flow panel method for two parent yacht hulls, each parameterized into 70 variants and evaluated at three speeds. ShipNet predicts per-point pressure coefficient and two-dimensional wave elevation map using a composite loss that combines point-wise regression and image-structure terms. On a geometry-held-out test set, ShipNet achieves R^2=0.98 for hull pressure and R^2=0.91 for wave fields. Inference requires approximately 0.15s per case, yielding over a 550x speedup relative to the potential-flow solver on conventional hardware. Limitations include the restricted geometry and speed ranges and the inviscid training data, while future work will extend the model to high-fidelity viscous simulations with physics-informed regularization.

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07.

arXiv (CS.CL) 2026-06-11 DOI: arXiv:2606.12342

ALIGNBEAM : Inference-Time Alignment Transfer via Cross-Vocabulary Logit Mixing

作者:

Chirag Chawla↗Pratinav Seth↗Vinay Kumar Sankarapu↗

Domain fine-tuning degrades the safety of large language models: fine-tuned specialists readily comply with harmful prompts framed in domain language. Existing inference-time defenses that mix logits from a safe anchor model require both models to share a vocabulary, which rules them out for the cross-family specialists where safety is most degraded. We present ALIGNBEAM, a training-free method that lifts this restriction by translating anchor logits into the target model's vocabulary token-by-token at each decoding step; a small LLM judge then selects the safest among K candidate continuations. No weights are changed, and the safety-utility trade-off can be tuned at deployment without retraining. Across both cross-vocabulary and same-vocabulary evaluation pairs, ALIGNBEAM substantially raises refusal on adversarial benchmarks while keeping task accuracy and inference overhead within practical bounds. The results show that safety alignment can be transferred between model families at inference time, without touching either model's weights.

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08.

arXiv (CS.CL) 2026-06-17 DOI: arXiv:2606.17819

A Framework for Evaluating Agentic Skills at Scale

作者:

Maksim Shaposhnikov↗Nicolas Fortuin↗Simon Stipcich↗Maria I. Gorinova↗Amy Heineike↗Rob Willoughby↗

Agent skills – structured, reusable knowledge artifacts that augment LLM agent capabilities – have been rapidly adopted in industry, yet their cross-domain impact and use across commercial and open-source models remain under-studied, and no reusable methodology exists for evaluating an individual skill. In this work, we present an evaluation framework that lets a skill author construct realistic tasks to rigorously assess the aspects of a skill that matter most to them, and that estimates skill utility by solving those tasks. Further, we apply our evaluation approach at scale to 500 real-world skills, generating 1,000 tasks derived from the skills' content, along with instruction-following and goal-completion scoring rubrics. Using these metrics, we evaluate how 19 agent-model configurations, both proprietary and open-source, perform on the tasks. Our results show that models vary widely in how closely they adhere to the instructions encoded in skills, leading to substantial differences in their performance gains. Furthermore, we show that access to a skill significantly changes model behavior compared to the no-skill setup, providing an essential mechanism for encoding opinionated workflows into LLM agents. We release our evaluation dataset to support future work on agent skills.

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09.

bioRxiv (Bioinfo) 2026-06-11 DOI: HASH:362612cc4a923d7b7d62582d58e5cc78

TMO: ASYMMETRIC CROSS-MODAL ATTENTION FOR LEARNINGCELL-STATE-DEPENDENT REGULATORY LAGS FROM SINGLE-CELL MULTIOMIC DATA

作者:

Lopez-Delgado↗P. A↗Delgado-Carlo↗M. M↗

Abstract Background: Single-cell multi-omics technologies simultaneously measure chromatin accessibility (ATAC) and gene expression (RNA), providing a unique window into the temporal ordering of regulatory events during differentiation. However, most computational models treat the two modalities symmetrically, ignoring the directional relationship between chromatin and transcription, and existing lag-aware methods estimate a single global lag per gene, failing to capture cell-state-dependent dynamics. Methods and Results: We introduce Temporal Multi-Omics (TMO), a deep learning framework that learns signed, cell-state-conditional regulatory lags ({Delta}{tau}) using asymmetric cross-modal attention. TMO projects RNA and ATAC into 50 latent components each, tokenises each cell as a sequence of 100 tokens, and uses a two-pass transformer in which a data-driven lag prior - derived from a sliding-window cross-correlation function - directly biases attention asymmetrically. On four independent 10x Multiome datasets (mouse brain, human brain, mouse kidney, human PBMC), the asymmetric model achieves Lag Concordance Scores (LCS) of 0.988-0.999, compared to 0.048-0.108 for an architecturally identical symmetric baseline. A stratified 80/20 held-out experiment confirms that the learned component-lag ordering generalises to unseen cells (held-out LCS 0.85-0.99). Clustered {Delta}{tau} heatmaps show positive {Delta}{tau} (ATAC-led priming) in early pseudotime and negative {Delta}{tau} (RNA-led, activity-dependent regulation) in late pseudotime; the ATAC-RNA correlation heatmap exhibits a U-shaped pattern indicative of developmental decoupling. Components with the most positive {Delta}{tau} are enriched for chromatin organization and stem cell differentiation (FDR < 0.05), while those with the most negative {Delta}{tau} are enriched for synaptic signalling and immune activation. Ablating the cell-state information from the lag predictor reduces the LCS and collapses per-component temporal dynamics (KS p [&le;] 0.039 in all four tissues), proving that TMOs dynamic lag patterns depend on cell-state conditioning. Independent ChIP-seq validation for four transcription factors (PAX5, Pax6, ASCL1, Hnf4) confirms highly significant separation between target genes and expression-matched background (p < 10-4 in all cases). Two Multiome Perturb-seq screens provide causal validation: SMARCB1 knockout shows a directional trend (1.5-fold target shift, p = 0.056, n = 147 perturbed cells), and SMARCE1 knockout reaches statistical significance (p = 0.0089, n = 3,394 perturbed cells). Gene-level cross-correlation independently validates that the regulatory lag signal is present in the raw data, and TMO further identifies rare, statistically significant biphasic gene programs where the regulatory direction reverses across pseudotime. Conclusions: TMO is the first method to make regulatory lag a learnable, cell-state-conditional, and architecturally encoded parameter. It is scalable, interpretable, and open-source, providing a powerful tool for studying regulatory timing in development, disease, and perturbation screens.

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10.

medRxiv (Medicine) 2026-06-11 DOI: HASH:1ca0b596491b006c73a0d32106621d33

Allostatic Load in Endometrial Cancer Disparities

作者:

Bey↗G. S↗Bowen↗M. B↗Wu↗Boykin↗Bernard↗Zhang↗Melendez↗Celestino↗Batsis↗J. A↗…

Background: Endometrial cancer incidence and mortality are increasing, particularly among Black women and for aggressive subtypes. Allostatic load (AL), a composite measure of physiologic dysregulation across metabolic, cardiovascular, and immune systems, varies by racial category and tumor subtype in other cancers. Endometrial cancer is strongly associated with obesity, and it is unknown whether AL scores maintain sufficient heterogeneity to evaluate differences across subgroups or with clinical outcomes. Objective: To describe the performance of AL scoring in endometrial cancer patients and examine associations with tumor characteristics (grade/histology) and survival outcomes. Methods: We evaluated AL among 398 participants newly diagnosed with endometrial cancer. AL score was calculated by assigning 1 point for each ''high-risk'' value (by clinical reference range or distribution-based) for 15 biologic variables for vital signs, anthropometrics, blood-based biomarkers, and medical comorbidities. Results: Distribution-based thresholds for variables were used to preserve heterogeneity in this obesity-dominant context. Overall, 68.7% of Black women had high AL compared to White (56.7%), Hispanic (56.7%), and other race (32.3%) women. Decision tree analyses revealed grade-dependent associations between AL and survival. For women with low-grade tumors, higher AL was associated with poorer overall survival. For high-grade tumors, intermediate AL ([&ge;]4,

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11.

arXiv (quant-ph) 2026-06-16 DOI: arXiv:2603.18374

Black Hole–Entropy Container or Creator

作者:

William G Unruh↗

arXiv:2603.18374v3 Announce Type: replace-cross Abstract: Do black holes possess entropy or do they create it? The dominant assumption is that they possess entropy, and a they evaporate that entropy is emitted and decreases. In this paper I use a model of a linear amplifier, in which I argue that the amplifier has not entropy and yet it emits entropy in the process of it operation. This model is closely related to behaviour of black holes, resulting in answer the question of that title that black holes do not have entropy, but nevertheless them create and emit entropy with the total entropy emitted being the same as the usual expression proportional to the square of the mass of the black hole.

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12.

arXiv (CS.LG) 2026-06-19 DOI: arXiv:2606.19411

Spectral DPPs via NEPv: A Scalable Continuous Relaxation of Determinantal MAP for Diversity-Aware Data Selection

作者:

Richard Yi Da Xu↗

arXiv:2606.19411v1 Announce Type: new Abstract: Selecting a small, diverse, high-quality subset from a massive pool of candidates is a recurring primitive in modern machine learning – data curation and coreset selection for training and fine-tuning large models, active-learning batch acquisition, prompt and exemplar selection for in-context learning, retrieval diversification, and experimental design. Determinantal Point Processes (\operatorname{DPP} s) give a principled, well-calibrated notion of diversity for this task, but their MAP objective – pick a size-$k$ subset $S$ maximizing $\logdet(L_S)$ – is NP-hard, and the standard greedy and sampling algorithms scale superlinearly in the ground-set size $n$. This cost is prohibitive precisely in the data-centric regime where diversity matters most, where $n$ ranges over millions to billions of candidate examples, features, or embeddings. We recast \operatorname{DPP}-MAP as a continuous optimization problem over the Stiefel manifold, and show that its first-order optimality conditions form a Nonlinear Eigenvalue Problem with eigenvector dependency (\operatorname{NEP}v) of a previously unstudied form. This \operatorname{NEP}v\ admits a self-consistent field (\operatorname{SCF}) iteration with a spectral-gap-based local contraction guarantee, giving a principled iterative solver where the diversity objective drives an eigenvector-dependent operator. The resulting algorithm, \OurMethod, requires only matrix-vector products with the kernel and runs in time $O\!\big((ndk+nk^2)\,t\big)$ for a small number of iterations $t$, scaling near-linearly in $n$ and integrating directly with low-rank and feature-map kernels common in ML. This paper focuses on the relaxation, solver, and scaling analysis; full real-data benchmarking is left to a planned empirical study.

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13.

arXiv (CS.LG) 2026-06-11 DOI: arXiv:2605.22346

The ASE-LSE Disagreement Landscape: An End-to-End Characterisation of Extremes and Structural Drivers

作者:

Minh Triet Pham↗Ian Gallagher↗

arXiv:2605.22346v3 Announce Type: replace-cross Abstract: Two of the most widely used methods for analysing graph data, Adjacency Spectral Embedding and Laplacian Spectral Embedding, often produce different results when applied to the same graph. Yet the structural reasons behind this disagreement remain incompletely understood. This paper provides an end-to-end account of ASE-LSE latent subspace disagreement. We first prove that the two methods produce identical latent subspaces for every embedding dimension whenever the Laplacian is a scalar multiple of the adjacency matrix, and show that this scalar relationship holds if and only if the graph is either regular or bipartite biregular. This anchor result identifies a sufficient condition for perfect agreement that pins down the floor of the disagreement spectrum and supplies the baseline for the perturbation analysis. We then prove that no maximal-disagreement graph or family of graphs exists: the disagreement is always strictly below its theoretical ceiling, and we exhibit a witness family demonstrating that no finite maximum is attainable, so the disagreement landscape has no maximiser. With both endpoints established, we derive a Regularity Departure Bound whose two terms isolate degree heterogeneity and eigengap as the primary structural factors influencing disagreement in the middle regime. Empirical validation across thousands of simulated graphs confirms the mechanisms predicted by the bound: heterogeneity pushes disagreement up, eigengap suppresses it, and their joint ratio emerges as a unified predictor of ASE-LSE disagreement, suggesting when the two embeddings can be treated as interchangeable and when they cannot.

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14.

arXiv (CS.LG) 2026-06-15 DOI: arXiv:2606.14463

EM-NeSy: Expectation Maximization for Neurosymbolic Learning

作者:

Annegret Seibt↗Luc De Raedt↗Giuseppe Marra↗

arXiv:2606.14463v1 Announce Type: new Abstract: Neurosymbolic (NeSy) models integrate neural networks and symbolic reasoning for robust and interpretable AI. State-of-the-art NeSy models require that the symbolic component is expressed in a differentiable way, often complicating the use of approximate inference. We propose EM-NeSy which casts probabilistic NeSy learning as an instance of the Expectation-Maximization (EM) algorithm. In the expectation step, we compute the posterior over the neurally predicted symbols conditioned on the label via probabilistic inference. In the maximization step, we update the neural parameters based on this posterior using gradient descent only through the neural component. This formulation unlocks the full potential of the EM algorithm for NeSy learning. It allows NeSy to extend naturally to approximate reasoning without any additional modifications or differentiability requirements of the symbolic component. Furthermore, it recovers the standard end-to-end gradient-based NeSy setting under exact inference. Our experimental results demonstrate the scalability and computational efficiency of EM-NeSy.

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15.

arXiv (CS.CV) 2026-06-18 DOI: arXiv:2406.18215

Optimizing Incomplete, Large-Scale and Sparse Multi-Graph Matching in Bioimaging

作者:

Max Kahl↗Sebastian Stricker↗Lisa Hutschenreiter↗Florian Bernard↗Carsten Rother↗Bogdan Savchynskyy↗

Multi-graph matching is a fundamental problem in computer vision. Our work is motivated by a challenging application in bioimaging, where dozens or even hundreds of 3D microscopy images of worms must be brought into correspondence. Existing datasets do not cover this large-scale regime, and virtually all existing methods are inapplicable because they assume a complete or dense problem setting. To support further research, our first contribution is a new large-scale dataset based on problem instances from bioimaging. Our second contribution is a comprehensive analysis of the two main multi-graph matching paradigms: direct and permutation synchronization-based formulations. We argue, in part by proof, that practical large-scale methods must explicitly address problem sparsity and incompleteness. Since standard permutation synchronization approaches fail in this setting, we further introduce a sparse permutation synchronization paradigm. Our final contribution is GREEDA, a general method for sparse and incomplete problems that can be instantiated across cost orders and paradigms. While our paper focuses on objective functions up to quadratic order, GREEDA is inherently generalizable to arbitrary orders. On larger, sparse instances, GREEDA outperforms competing methods in both objective value and runtime. For example, for moderately-sized problems based on 30 worm images GREEDA produces a high-quality solution within 2 minutes, whereas competitors require at least half an hour and yield far worse results. On smaller dense problems, GREEDA remains on par with leading methods while being an order of magnitude faster.

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16.

arXiv (CS.CL) 2026-06-18 DOI: arXiv:2606.18284

Breaking the Solver Bottleneck: Training Task Generators at the Learnable Frontier

作者:

Lorenz Wolf↗Connor Watts↗Roger Creus Castanyer↗Geoffrey Bradway↗Maxwill Lin↗Augustine N. Mavor-Parker↗Matthew Daborn-Sargent↗

The limiting resource for training agents via reinforcement learning (RL) is increasingly frontier task supply: valid, solvable tasks just difficult enough to train the current model. As reasoning and agentic models improve, fixed task distributions saturate, while naive synthetic generation yields tasks that are trivial, impossible, or ill-posed. Training a task generator with RL to optimize validity and learnability can address this bottleneck, but direct optimization requires repeated solver rollouts per candidate. For software-engineering (SWE) tasks, a single rollout can take tens of minutes; solver-in-the-loop generator training is intractable. We introduce PROPEL, a solver-amortized framework for training task generators at the targeted solve rate. PROPEL trains a lightweight activation probe on a one-time labeled corpus of generated tasks and solver outcomes. The probe predicts target-solver pass rate from a frozen generator reference model and serves as a proxy for solve rate during generator optimization, reducing generator evaluation to a single forward pass. Across math, code, and software-engineering at multiple model scales, PROPEL shifts generation toward the targeted solve rate: for coding, tasks generated at the learnable frontier increase from $10.1\% \rightarrow 20.0\%$ for a Qwen2.5-3B-Instruct solver and from $5.3\% \rightarrow 12.6\%$ for a Qwen2.5-7B-Instruct solver. For SWE, PROPEL increases the share of generations at the targeted solve rate from $9.8\% \rightarrow 19.6\%$ for Qwen3.5-27B on repositories not seen during training of probe and generator.

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17.

arXiv (CS.LG) 2026-06-18 DOI: arXiv:2606.18857

Investigating Inductive Biases for Machine Learning Emulation of Sudden Stratospheric Warmings in Idealised Isca Simulations

作者:

Oskar Bohn Lassen↗Simon Driscoll↗Stephen I. Thomson↗Sebastian Schemm↗Francisco C. Pereira↗

arXiv:2606.18857v1 Announce Type: new Abstract: Machine-learning emulators are increasingly used for weather prediction and have the potential to extend skill on subseasonal-to-seasonal timescales by learning dynamically important sources of predictability. A key challenge is whether the models can exploit predictability anchors, such as stratospheric variability, that influence tropospheric circulation beyond short lead times. We test how architectural inductive bias affects emulation of sudden stratospheric warming (SSW) dynamics using paired idealised Isca simulations that differ only in an imposed wave-2 heating perturbation. Across convolutional, transformer, and graph-based architectures trained for one-step prediction, model differences are modest when the stratosphere is dynamically quiet but widen substantially when SSW-like variability is active. Our results identify explicit three-dimensional vertical coupling as a key inductive bias for machine-learning emulation of stratospheric dynamics. However, Eliassen-Palm flux diagnostics show that low forecast error does not guarantee physically faithful wave-mean-flow interaction, with coherent errors remaining in stratospheric wave-driving structure.

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18.

arXiv (CS.CV) 2026-06-16 DOI: arXiv:2606.15592

DenseControl: Instance-Level Controllable Synthesis of Dense Crowd Image

作者:

Juncheng Wang↗Lei Shang↗Wang Lu↗Baigui Sun↗Shujun Wang↗

In this paper, we introduce DenseControl, a novel pipeline for generating dense crowd images. Specifically, DenseControl meticulously positions and sizes each generated instance to align precisely with the predefined coordinates and scales. Based on this, we further allow for control over the background, style, and attributes of instances. The motivation behind DenseControl stems from the observation of two main challenges in synthesizing crowd images: controlling signal embedding and maintaining topological integrity when imparting instance scale guidance. To address these, we first introduce the Isolated Object Embedding (IOE) map, a novel representation that facilitates spatial location control while mitigating the difficulties associated with learning projections for model. Secondly, we propose an Implicit Scale Embedding (ISE) strategy that seamlessly integrates with the IOE map to encode precise scale information. To further enhance the efficacy of combining ISE with the IOE map, we incorporate a Position Shortcut mechanism that enhances cross-attention to alleviate projection challenges. We evaluate DenseControl through two lenses: synthesis quality and applicability in latent applications. Experiments across different control conditions demonstrate DenseControl achieves state-of-the-art results in dense crowd image synthesis. Furthermore, we showcase applications in augmenting crowd analysis under data scarcity, transfer learning, and weather generalization scenes, to highlight the practical utility of DenseControl. The codebase will be released.

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19.

arXiv (CS.CV) 2026-06-16 DOI: arXiv:2606.16067

Stepwise Token Selection for Efficient Multimodal Large Language Models

作者:

Landi He↗Shawn Young↗Lijian Xu↗

In multimodal large language models (MLLMs), inference cost is largely dominated by the visual token prefix rather than the language backbone, making token reduction a key factor for improving efficiency. Existing approaches typically assign independent importance scores to visual tokens and retain a fixed number of top-ranked tokens, implicitly assuming token independence and a uniform compression ratio across inputs. In this work, we reformulate visual token pruning as a sequential decision-making process. Specifically, we introduce a pointer-style selection mechanism that iteratively chooses informative tokens, conditioning each decision on previously selected ones, and dynamically determines when to stop via a learned termination action. This enables joint optimization of both the selected subset and its size. To enable end-to-end training under standard language modeling objectives, we design a differentiable relaxation based on a variance-preserving noise interpolation scheme, allowing gradients to propagate through the discrete selection process. Extensive experiments on LLaVA-v1.5-7B and Qwen2.5-VL-7B demonstrate that our approach consistently outperforms fixed-ratio baselines across different compression levels. Under aggressive pruning that removes 88.9% of visual tokens, our method preserves 94.6% of the original accuracy while achieving a 1.88x speed-up in prefill latency.

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20.

medRxiv (Medicine) 2026-06-15 DOI: HASH:ca0df469f0e50db3973b6b49a4680a2e

Two Blood-based Endotypes Reveal Divergent Clinical Outcomes of Fibrotic Hypersensitivity Pneumonitis

作者:

Huang↗Ma↗S.-F↗Kim↗J. S↗Strickland↗Receveur↗B. A↗Bonham↗C. S↗Paul↗T. K↗…

Rationale: Fibrotic hypersensitivity pneumonitis (fHP) is an antigen-driven, life-threatening interstitial lung disease characterized by heterogeneous radiologic features, clinical outcomes, and treatment responses. Objectives: To identify blood-based fHP endotypes that inform mechanism, prognosis and therapeutic response. Methods: We performed integrative analyses of multi-compartment transcriptomic data derived from whole blood, peripheral blood mononuclear cells, bronchoalveolar lavage, and surgical lung biopsies, alongside circulating plasma proteomics. Multiple clustering algorithms were cross-compared to ensure robustness and reproducibility of endotypes identification. Immune cell composition was inferred using bulk RNA-seq deconvolution and annotated with BAL single-cell RNA-seq. Pathway activities were characterized using Gene Set Enrichment Analysis. Transplant-free survival (TFS) was evaluated for endotype and corticosteroid exposure by Kaplan-Meier methods, with hazard ratios analyzed using multivariable Cox proportional hazards models. Results: Two molecular endotypes, lymphocytic-associated (L-fHP) and non-lymphocytic-associated (N-fHP), were identified and validated. L-fHP showed enrichment of adaptive immune signaling and lymphocyte predominance, whereas N-fHP demonstrated myeloid-cell activation with neutrophil and macrophage predominance. Corticosteroid exposure was associated with worse TFS in L-fHP but not in N-fHP after adjusting for age, sex, and baseline pulmonary function. Compared to L-fHP, N-fHP had poorer baseline pulmonary function, faster 12-month FVC decline, and shorter TFS. N-fHP also exhibited elevated neutrophil-associated markers, including matrix metalloproteinase-9, across paired transcriptomic and proteomic datasets, supporting a neutrophil-driven, cross-compartment disease process. Conclusion: Multi-omic, multi-compartment analysis identifies two reproducible fHP endotypes with distinct clinical outcomes and corticosteroid responses, supporting a precision medicine approach beyond current clinical and radiologic classification.

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21.

arXiv (CS.CV) 2026-06-16 DOI: arXiv:2606.14758

Disentangling Hallucinations: Orthogonal Semantic Projection for Robust Interpretability

作者:

Emirhan Bilgi\c{c}↗Baptiste Caramiaux↗Zhi Yan↗Gianni Franchi↗

As Vision-Language Models are increasingly deployed in safety-critical applications, the trustworthiness of their explanations becomes crucial. Explainable AI (XAI) methods for Vision-Language Models often suffer from semantic hallucination, where attribution maps highlight prominent image regions even when prompted with incorrect text descriptions (e.g., highlighting a dog when prompted ``cat''). Although this problem is widespread, a formal mathematical analysis of XAI methods and CLIP embeddings is largely missing in the literature. We demonstrate that this phenomenon is not specific to a single architecture but is a fundamental consequence of Linear Semantic Leakage in high-dimensional embedding spaces. We propose a unified theoretical framework, Linear Semantic Attribution (LSA), which generalizes across discriminative methods. We introduce OSP, a geometric intervention that utilizes the residual property of OMP to disentangle unique semantic signals from shared concepts. We prove theoretically and demonstrate empirically that OSP minimizes hallucination by orthogonalizing the query vector against distractor concepts, rendering the attribution model blind to shared features while preserving fidelity for correct prompts. Our code is available at: https://github.com/emirhanbilgic/Orthogonal-Semantic-Projection

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22.

arXiv (CS.AI) 2026-06-17 DOI: arXiv:2606.17648

From Brewing to Resolution: Tracing the Internal Lifecycle of Code Reasoning in LLMs

作者:

Siyue Chen↗Yifu Guo↗Yuquan Lu↗Zishan Xu↗Jiaye Lin↗Jianbo Lin↗Siyu Zhang↗Cheng Yang↗Junxin Li↗Yujia Li↗Yu Huo↗Ruixuan Wang↗…

arXiv:2606.17648v1 Announce Type: new Abstract: Standard accuracy metrics cannot explain why LLMs handle variable tracking but fail on semantically equivalent loops. We study an internal lifecycle of code reasoning in which models first brew the answer, making it linearly recoverable many layers before it becomes self-decodable, and then diverge into one of four resolution outcomes: Resolved, Overprocessed, Misresolved, or Unresolved. Understanding this lifecycle matters because similar task accuracies can mask fundamentally different failure modes that surface-level evaluation cannot detect. We introduce a dual diagnostic framework pairing layer-wise linear probing with Context-Stripped Decoding (CSD) and apply it to six code-reasoning task families across 16 models spanning Qwen, Llama, and DeepSeek architectures. All four outcomes carry substantial mass in every task family: overall Resolved is only 41.5%, with multiple tasks below 30%. Controlled sweeps over structure, depth, and operators expose task-specific failure bottlenecks: Function Call Resolved plunges from 61.1% to 2.5% as call depth increases from one to three. Across architectures and scales, the brewing scaffold remains stable, with normalized brewing duration 24-42% across all 16 models, while resolution success varies with capability. This indicates that the scaffold is a stable empirical regularity across the tested decoder-only Transformer families, whereas resolution success covaries with capability, scale, and training. Code: https://github.com/euyis1019/llm-brewing

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23.

arXiv (CS.LG) 2026-06-11 DOI: arXiv:2606.11304

SPADE: Split-and-Delay Embeddings for Autoregressive High-Granularity Calorimeter Simulation

作者:

Joschka Birk↗Frank Gaede↗Anna Hallin↗Gregor Kasieczka↗Martina Mozzanica↗Henning Rose↗

arXiv:2606.11304v1 Announce Type: cross Abstract: We introduce SPADE (SPlit And Delay Embeddings), an autoregressive transformer for sequences whose tokens carry multiple features. Rather than embedding these features jointly, SPADE embeds them independently. Delaying each feature stream relative to the previous one allows intra-token correlations to be learned by the standard self-attention mechanism. Applied to point-cloud calorimeter shower generation in the highly granular ILD detector, SPADE is competitive with the state of the art AllShowers model on photon showers, and substantially outperforms its VQ-VAE-based predecessor OmniJet-$\alpha_C$. The mechanism is applicable to any generative task with multi-feature tokens, enabling LLM-style pretraining workflows for higher-dimensional data.

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24.

medRxiv (Medicine) 2026-06-15 DOI: HASH:0efee22e896d007187f998cdafed6089

Socioeconomic inequalities in smoking prevalence and intensity in Germany: A repeated cross-sectional analysis from 1998 to 2024

作者:

Emmert-Fees↗K. M. F↗Meyer↗Laxy↗Hanselmann↗

Background: Smoking inequalities by socioeconomic status have widened consistently in Germany, but sex-specific trends after 2013 and inequalities in daily cigarette consumption among smokers (intensity) are unknown. We analyzed trends in absolute and relative socioeconomic inequalities in smoking prevalence and intensity among German adults across three decades. Methods: We used 14 waves (1998-2024) of population-representative cross-sectional data from the German Socio-Economic Panel to estimate sex-specific trends in smoking prevalence and intensity in adults aged 25-64. Inequalities were quantified across strata of education, occupation, and equivalized household income using the absolute and relative concentration index with 95% bootstrap confidence intervals. Results: Overall smoking prevalence declined from 35.05% (CI: [33.90%, 36.20%] in 1998 to 22.19% (CI: [21.15%, 23.24%]) in 2024, and mean intensity from 17.49 (CI: [17.09,17.90]) to 13.33 (CI: [12.88, 13.79]) cigarettes/day. Over this period sex-differences in both outcomes narrowed almost completely. Absolute and relative inequalities in smoking prevalence widened across all SES dimensions, particularly for education and occupation. By 2024, inequalities were larger among women than men driven by a stagnating or rising smoking prevalence among low-SES women at least until 2018 alongside continued declines in higher-SES women and for men. Inequalities in smoking intensity, particularly related to income, were generally smaller than those in prevalence. Conclusion: Socioeconomic smoking inequalities in Germany widened from 1998 to 2024 primarily driven by reductions among higher-SES groups and increases in low-SES women. However, recent reductions in low-SES women may indicate a new phase in the smoking epidemic. Health equity considerations should be integrated into a targeted German tobacco control strategy.

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25.

arXiv (CS.LG) 2026-06-19 DOI: arXiv:2606.19416

MortarBench: Evaluating Mortgage Loan Origination Agents

作者:

Matthew Toles↗Yunan Lu↗Manav Munjal↗Bojun Liu↗Yuanhao Deng↗Stephanie Selig↗Derek Rindner↗Cheng Li↗Zhou Yu↗

arXiv:2606.19416v1 Announce Type: new Abstract: Loan origination is the process by which a lender creates a new loan, from application and underwriting through approval and funding. This process serves a critical role in evaluating the eligibility and level of risk posed by an applicant. Recently, firms have begun using mortgage loan agents to augment human loan officers, despite a lack of any public benchmark. To fill this gap, we present MortarBench, a loan origination agent benchmark. MortarBench uses a financial data synthesis and mutation pipeline to generate examples with broad edge case coverage that match real-world distributions and questions. We find that state-of-the-art large language models (LLMs) perform poorly, with closed-source models achieving at most 77.1\% exact match accuracy. We also discover systematic biases in LLM perception of foreignness related to non-English names. Noting these weaknesses, we introduce CRIT, a confidence calibration framework. Our method increases accuracy to 80.5\% while improving risk management steering and reducing bias.

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